It was probably lost ... why don't you pay online instead ... instant receipt ... https://www.ftb.ca.gov/pay/
I highly recommend to all my clients to use electronic payment methods for taxes. For those that are scared that for some reason the IRS or other tax authorities will seize their account I remind them that the routing number and account number are on checks which is all the info needed. People can pay by money orders or bank checks (cashiers, etc ) but if they get lost in the mail and if receipt is lost or misplaced, trying to prove payment may be impossible as well as trying to get money back if check is never cashed.
every tax authority that allows electronic payment also allows printing of receipt with unique identifying number to trace if needed but you do need to save it as needed. many of these sites will also allow you to look up these payments, cancel before payment date and perform other activities. even extension payments can be made this way
Agreeing with @Critter for the future, suggest you call the CA franchise Tax board and confirm if they have received the check. If yes, do not worry and if NO, then cancel the check ( stop payment ) at your bank and then follow CRitter's suggestion of paying at CA Franchise Tax Board's site -- it is quite safe ( they can direct debit from your account).